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how to normalize microarray expression set

I have downloaded a database from GEO using getGEO and then converted it into ExpressionSets using GDS2eSet. Now I am trying to normalize it using rma. It gives me error :unable to find an inherited method for function ‘probeNames’ for signature ‘"ExpressionSet". Which function I showed use to normalize the expression set ?

a1<-getGEO('GDS4758',  destdir=".")
eset<- GDS2eSet(a1, do.log2=TRUE)
eset1<-rma(eset)

gds getgeo rma

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updated 7.4 years ago by Kevin Blighe

• written 8.8 years ago by Michel Edwar

The platform for GDS4758 is GENE ST array. For ST array normalization 'oligo' package is used. So e.rempel's suggestion below should work. Check this webpage http://homer.ucsd.edu/homer/basicTutorial/affymetrix.html (see "Newer Affymetrix Arrays (Gene ST arrays, etc.")

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written 8.8 years ago by Diwan

1 answer

Hi,

the error message resembles one in this thread. It looks like you should use different rma function, namely from oligo package. You could try oligo::rma instead of rma (after possible installation of oligo library)

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written 8.8 years ago by e.rempel

Indeed, for ST arrays, you should use the oligo package, not affy

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written 7.4 years ago by Kevin Blighe

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